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Innotargets: Introduction to Metabolic Modelling

DRAFT/UNDER CONSTRUCTION STUDENTS PLEASE IGNORE

Barcelona 2023

Tutors

Mark Poolman (MP: Oxford Brookes University)
Oliver Ebenhoeh (OE: Heinrich Heine University, Dusseldorf)
Yanica Said (YS: Oxford Brookes University)
Dipali Singh (DS: Quadram Institute, Norwich)
Hester Chapman (HC: University of Nottingham)

Guest Speaker ??

TBA ??

Reading List ??

Suggestions ?

Course Timetable and Resources

Day	Time	Activity	Links	Lecturer
Tuesday	AM
03/04/22	09:00	Arrival, Admin & Registration
	PM
	12:00	Lunch
	13:00	Welcome and introduction to the course. Outline of the week.		MP et al
		Lecture 1: Who? What?	Slides	???
		Lecture 2: Introduction to metabolic modelling. Mathematical representation of metabolic networks.	Slides	DS
		Tea/coffee
		Lecture 3: Python and computational representation of metabolic networks.	Slides	MP
		P1. Computers: checking internet connectivity, software installation.	Installation of ScrumPy.	All
		Close
Wednesday	AM
	09:00	P2. Python and ScrumPy	Prac2	All
		Lecture 4: Null space, subsets and elementary modes	Slides	MP
	11:00	Break
		P3. Null space, subsets and elementary modes	Prac3	All
	13:00	Lunch + Social Acitivity - visit to the Sagrada Familia
	PM	Lecture 5. Biotechnological applications of elementary modes analysis	Slides	DF
		P4. Elementary Modes of the Woods-Ljungdahl Pathway	Prac4	All
Thursday
	09:00	Lecture 6: Linear programming and Flux Balance Analysis	Slides	MP
		Lecture 7 : Validation and construction of models	Slides	DS
	11:00	Break
		Lecture 8: Determination of minimal media requirements for Campylobacter jejuni	Slides	DS
		P5: Determination of minimal media requirements for Campylobacter jejuni	Prac5	DS
	13:00	Lunch
	PM	Lecture 9: Phaeodactylum tricornutm for biofuel synthesis	Slides	DS
		P6. Identifying pathways for TAG synthesis in P. tricornutm	Prac6	All
	16:45	close

None: Meetings/Barcelona2023/Timetable (last edited 2023-05-29 12:34:39 by mark)

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-Deletions are marked like this.
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-DRAFT/UNDER CONSTRUCTION STUDENTS PLEASE IGNORE
+== DRAFT/UNDER CONSTRUCTION STUDENTS PLEASE IGNORE ==
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+Line 6:
- * David Fell        (DF: Oxford Brookes University)
+ * Oliver Ebenhoeh (OE: Heinrich Heine University, Dusseldorf)
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+Line 9:
- * Nicole Pearcy  (NP: University of Nottingham)
+ * Hester Chapman (HC: University of Nottingham)
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-== Guest Speaker ==
 * Prof. John Wain  (JW: Quadram Institute, Norwich)
+== Guest Speaker ?? ==
 * TBA ??
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+Line 14:
-== Reading List ==
 . A reading list for topics covered in the course is provided [[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Reading|here]] (updated).
+== Reading List ?? ==
 . Suggestions ?
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-|| || ||Lecture 1: Young microbiologists need models not critics ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L1.pdf|Slides]] ||JW ||
|| || ||Lecture 2:  Introduction to metabolic modelling.   Mathematical                     representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||DF ||
+|| || ||Lecture 1: Who? What? ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L1.pdf|Slides]] ||??? ||
|| || ||Lecture 2:  Introduction to metabolic modelling.   Mathematical                     representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||DS ||
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-|| ||13:00 ||Lunch || || ||
+|| ||13:00 ||Lunch + Social Acitivity - visit to the Sagrada Familia || || ||
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-||Friday          ''' ''' ||AM          ''' ''' || || || ||
|| ||09:00 ||Lecture 10. ''Cupriavadus necator''        ''' ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L10.pdf|Slides]] ||NP ||
|| || ||P6 (ctd) P7: KOs for ethelene production in ''C. necator'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P7|Prac7]] || ||
|| ||13:00 ||Lunch || || ||
|| ||14:00 ||Concluding remarks, discussion, feedback || || ||
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+|| || || || || ||
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